The repository contains all the material required to reproduce the figures in the article:
Vanderaa, Christophe, and Laurent Gatto. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” arXiv [q-bio.QM]. arXiv. http://arxiv.org/abs/2304.06654.
This image is licensed under a Creative Commons Attribution 4.0 International License.
make_figure[1234].R: 4 scripts that produce the article's figures, each figure being generated by a separate script.utils.R: an R script with functions used by the scripts above.install_dependencies.R: an R script that installs all the required dependency packages.figs/: folder containing the generated figures.Dockerfile: the instructions used to build the Docker image.
Each figure is generated in its own script. We garantee long term
reproducibility by relying on Docker. You must first install
Docker on your local machine. Then, pull the image from the
DockerHub
repository.
docker pull cvanderaa/2023_scp_na_docker
Then clone this repository on your local machine:
git clone [email protected]:UCLouvain-CBIO/2023_scp_na
cd 2023_scp_na/
Start an Rstudio session within a Docker container using:
docker run -e PASSWORD=bioc -p 8787:8787 -v `pwd`:/home/rstudio/ cvanderaa/2023_scp_na_docker:latest
Note you should use %CD% instead of pwd when using Windows.
Open your browser and go to http://localhost:8787. The USER is
rstudio and the password is bioc. See the DockerHub
repository
for more detailed information on getting started with Docker.
(I don't think I'll ever have to rebuild the image, but who knows).
Build the image (make sure to cd in the 2023_scp_na local repo):
docker build -t cvanderaa/2023_scp_na_docker .
When complete, push the new image to DockerHub:
docker push cvanderaa/2023_scp_na_docker
To reuse the code for publications, please cite:
Vanderaa, Christophe, and Laurent Gatto. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” arXiv [q-bio.QM]. arXiv. http://arxiv.org/abs/2304.06654.
The code is provided under a permissive Artistic 2.0 license.